Analysis of urban sewage SARS-CoV-2 monitoring results in Guiyang city in 2023.

Objective To investigate the concentration and genetic variations of SARS-CoV-2 in sewage in Guiyang city from February to December 2023. Methods A total of 1 034 sewage samples were analyzed for ORFlab and N gene concentrations using quantitative PCR, and full viral genome sequencing was performed using the Illumina sequencing platform. Results Among the 1 034 samples collected, 587 were tested positive for SARS-CoV-2. The median concentration of the ORFlah gene was 3.69 copies/ml, and the median concentration of the N gene was 7.57 copies/ml. There was a correlation between the concentration of SARS-CoV-2 in sewage and the number of reported cases from medical institutions. Full genome sequencing was conducted on five SARS-CoV-2 positive samples with CT values <32, achieving an average coverage ranging from 63.91% to 97.28%. All viral types identified were Omicron sub lineages, with a total of 110 mutation sites identified. The S protein exhibited 22 amino acid changes, including the critical mutation E484A. Conclusion The detection rate of SARS-CoV-2 in urban sewage in Guiyang city is relatively high, and the viral concentration correlates well with clinical cases. The application of whole genome sequencing technology allows for the detection of genetic variants in the viral material present in sewage and identifies multiple mutation sites. Monitoring viruses in urban sewage effectively captures the spatiotemporal trends of the disease, serving as an important complement to clinical testing and providing a reference for local governments to implement precise epidemic prevention policies. [ABSTRACT FROM AUTHOR]